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One of the current challenges facing biologists is the discovery of novel functional elements in noncoding genomic sequence. With the rapidly increasing number of genomes being sequenced, a comparative genomics approach called ‘phylogenetic footprinting’ has become a favored method for such discovery. The idea underlying phylogenetic footprinting is that selective pressure causes functional elements to evolve at a slower rate than the nonfunctional surrounding sequence. Therefore the most conserved motifs in a collection of homologous regions are excellent candidates as functional elements.
(Neph., 2006) MicroFootPrinter: a tool for phylogenetic footprinting in prokaryotic genomes. Nucleic Acids Res.